Nucleic acids (DNA and RNA) can be synthesized chemically or enzymatically. Chemical synthesis of nucleic acids can be achieved without a template, i.e., with only the in silico knowledge of the sequence, but the length of the synthesized fragments in practice is limited to about 100 to 200 base pairs due to side reactions (e.g., depurination, branching, etc.) and coupling efficiencies less than 100%. In addition, the end product is a mixture of the intended sequence and of sequences with multiple random deletions. On the other hand, enzymatic synthesis allows generation of long fragments (more than 1000 bases) but requires a template of the sequence to reproduce. The purity is usually high and errors are typically mutations due to the incorporation of the wrong base by the enzyme(s) used.
Recently, considerable interest has been shown in achieving the synthesis of long pieces of nucleic acids without the use of a template, such as in gene synthesis applications. This approach offers the advantages of both chemical and enzymatic synthesis, without the drawbacks of both. For example, Cello, et al., Science 2002; 297:1016-18, report that they were able to synthesize long parts of the polio virus without physical access to the natural template, i.e., solely from electronic sequence information and commercially available DNA oligonucleotides. More recently, Church, et al., Nature 2004; 432:1050-54, have shown that such gene synthesis was indeed possible using nucleic acids manufactured on a microarray platform.
Cleaving oligonucleotide probes off of an array substrate may facilitate gene synthesis. However, in certain cases, it may be desirable to control the applications to which an array platform is put and to limit the use of an array in gene synthesis reactions. For example, in certain instances, a supplier may desire to provide an array for limited use in particular applications (e.g., such as in diagnostic assays) for which the supplier may be able to provide quality assurances.